Pan tissue transcriptome analysis of long noncoding rnas in the american beaver castor canadensis

We thus identified 187 putative lncRNAs in the beaver transcrip-tome, of which 147 appear to be novel and 40 are ortho-logs of known noncoding transcripts in other species, such as XIST,

R E S E A R C H A R T I C L E Open Access

Pan-tissue transcriptome analysis of long

noncoding RNAs in the American beaver

Castor canadensis

Amita Kashyap1, Adelaide Rhodes2, Brent Kronmiller2, Josie Berger3, Ashley Champagne3, Edward W Davis2, Mitchell V Finnegan5, Matthew Geniza6, David A Hendrix7,8, Christiane V Löhr1, Vanessa M Petro3,

Thomas J Sharpton9,10, Jackson Wells2, Clinton W Epps4, Pankaj Jaiswal6, Brett M Tyler2,6and

Stephen A Ramsey1,8*

Abstract

Background: Long noncoding RNAs (lncRNAs) have roles in gene regulation, epigenetics, and molecular

scaffolding and it is hypothesized that they underlie some mammalian evolutionary adaptations However, for many mammalian species, the absence of a genome assembly precludes the comprehensive identification of lncRNAs The genome of the American beaver (Castor canadensis) has recently been sequenced, setting the stage for the systematic identification of beaver lncRNAs and the characterization of their expression in various tissues The objective of this study was to discover and profile polyadenylated lncRNAs in the beaver using high-throughput short-read sequencing of RNA from sixteen beaver tissues and to annotate the resulting lncRNAs based on their potential for orthology with known lncRNAs in other species

Results: Using de novo transcriptome assembly, we found 9528 potential lncRNA contigs and 187 high-confidence lncRNA contigs Of the high-confidence lncRNA contigs, 147 have no known orthologs (and thus are putative novel lncRNAs) and 40 have mammalian orthologs The novel lncRNAs mapped to the Oregon State University (OSU) reference beaver genome with greater than 90% sequence identity While the novel lncRNAs were on average shorter than their annotated counterparts, they were similar to the annotated lncRNAs in terms of the relationships between contig length and minimum free energy (MFE) and between coverage and contig length We identified beaver orthologs of known lncRNAs such as XIST, MEG3, TINCR, and NIPBL-DT We profiled the expression of the 187 high-confidence lncRNAs across 16 beaver tissues (whole blood, brain, lung, liver, heart, stomach, intestine, skeletal muscle, kidney, spleen, ovary, placenta, castor gland, tail, toe-webbing, and tongue) and identified both tissue-specific and ubiquitous lncRNAs

Conclusions: To our knowledge this is the first report of systematic identification of lncRNAs and their expression atlas in beaver LncRNAs—both novel and those with known orthologs—are expressed in each of the beaver tissues that we analyzed For some beaver lncRNAs with known orthologs, the tissue-specific expression patterns were phylogenetically conserved The lncRNA sequence data files and raw sequence files are available via the web supplement and the NCBI Sequence Read Archive, respectively

Keywords: lncRNA, Beaver, Transcriptome, Long noncoding RNA, Castor canadensis, Expression atlas

© The Author(s) 2020 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made The Creative Commons Public Domain Dedication waiver

* Correspondence: stephen.ramsey@oregonstate.edu

1

Department of Biomedical Sciences, Oregon State University, Corvallis, OR,

USA

8 School of Electrical Engineering and Computer Science, Oregon State

University, Corvallis, OR, USA

Full list of author information is available at the end of the article

Long noncoding RNAs (lncRNAs)—functional

ribo-nucleic acids that do not encode proteins and are at least

200 nucleotides (nt) in length [1]—regulate gene

expres-sion through diverse mechanisms including epigenetic,

chromatin, and molecular scaffolding interactions For

example, the primary effector for X-chromosome

inacti-vation, XIST, is a lncRNA [2] More broadly, various

noncoding RNAs (ncRNAs) have been implicated in host

defense against specific pathogens and in responses to

various stressors, including hypoxia [3,4] Mounting

evi-dence implicating species-specific ncRNAs and gene

regulatory mechanisms in species adaptations [3, 5],

in-cluding various species-specific responses to hypoxia [3,

4], suggests that species-specific and taxon-specific

lncRNAs may underlie some of the adaptations seen in

mammalian evolution However, out of more than five

thousand extant mammalian species (estimated as of

2019), less than 90 have high-quality genome assemblies

available (according to the Ensembl genome database [6]

release 96), and for those that do not, the absence of a

genome or transcriptome sequence precludes

compre-hensive sequencing-based identification of lncRNAs

The genome and three tissue transcriptomes of the

American beaver Castor canadensis (Order Rodentia,

Family Castoridae) have recently been sequenced [7, 8],

enabling the systematic search for molecular

determi-nants of this semi-aquatic herbivore’s unique

example, the beaver’s ability to hold its breath for up to

fifteen minutes [9] suggests adaptations in the brain,

heart, liver, and lungs to mitigate hypoxia-associated

tis-sue damage and optimize oxygen uptake [10] The

bea-ver’s abilities to digest tree bark [11] and certain toxic

plants [12] may depend on adaptations of detoxifying

enzymes [13,14] and lignocellulose-catabolizing gut

mi-crobes [15] Such enzymatic adaptations may involve

novel lncRNAs Indeed, lncRNAs have been implicated

in species-specific adaptations such as hibernation in

grizzly bears [16] and adaptation to cold in zebrafish

[17] Therefore, establishing a compendium of beaver

lncRNAs (both novel lncRNAs and those that are

ortho-logous to known lncRNAs in other species) is an

import-ant starting point for efforts to understand the roles of

noncoding RNAs in regulating expression of genes that

underlie beaver anatomy and physiology

Current high-throughput approaches for

transcrip-tome profiling—especially for species for which only a

draft reference genome is available—typically produce a

fragmented transcriptome [18] As a result, in the

ab-sence of an annotated genome, delineating a lncRNA

transcript from a noncoding portion of a protein-coding

transcript poses a bioinformatics challenge Because a

lncRNA is defined by not encoding a protein product, it

is not possible to definitively identify a potential lncRNA

by isolating a novel protein product, as is the case with

an mRNA Furthermore, lncRNAs often have weak se-quence similarity across species [19], and the catalogue

of validated lncRNAs outside of model vertebrates (hu-man, mouse, rat) is incomplete However, computational tools are now available for accurately scoring a tran-script’s coding potential based on its sequence (e.g., lon-gest ORF and hexamer usage bias [20]), closing a key informatics gap for lncRNA discovery

We report on the first effort (of which we are aware)

to systematically identify and map polyadenylated lncRNAs in the American beaver Our rationale for

non-polyadenylated lncRNAs) is twofold: (1) biologically, the majority of functional lncRNAs reported to date are polyadenylated [21] and polyadenylated lncRNAs in gen-eral are expressed at higher abundances than non-polyadenylated lncRNAs [22]; and (2) from a technical standpoint, use of poly-A selection enables strand-specific transcript profiling and avoids the requirement

to validate (and ascertain the biases introduced by) the use of ribosomal RNA (rRNA) probe reagents in a spe-cies for which the reagents have not previously been tested [23] As the foundation for this effort, we used the recently-released Oregon State University beaver gen-ome assembly (see Methods) and we acquired and ana-lyzed high-throughput, short-read polyadenylated RNA sequence data from 16 beaver tissues We designed and implemented a computational analysis software pipeline for (1) assembling a pan-tissue beaver transcriptome; (2) identifying candidate lncRNA contigs based on evidence for coding potential and annotations of orthologous genes; and (3) measuring expression levels of the lncRNA contigs in the 16-tissue atlas We identified

9528 potential lncRNA contigs which we then more stringently filtered by computational assessment of cod-ing potential in order to minimize the number of codcod-ing transcripts erroneously identified as lncRNAs We thus identified 187 putative lncRNAs in the beaver transcrip-tome, of which 147 appear to be novel and 40 are ortho-logs of known noncoding transcripts in other species, such as XIST, MEG3, TINCR, and NIPBL-DT From the measured expression levels of the 187 lncRNAs across the 16 tissues, we (i) identified both tissue-specific and tissue-ubiquitous lncRNAs, (ii) correlated tissue expres-sion profiles of three beaver lncRNAs with the tissue ex-pression profiles of their orthologs and (iii) identified biological pathways and biological processes that beaver lncRNAs may regulate These results lay the groundwork for studying the cellular and biochemical mechanisms underlying the beaver’s unique physiology and provide

an analysis approach that can be used in lncRNA studies

in other species

Screening pipeline

In order to obtain a comprehensive profile of the

non-coding transcriptome of the American beaver, we

paired-end sequenced polyadenylated RNA pooled from

samples of sixteen different beaver tissues and de novo

transcriptome using Trinity (see Methods) We merged

the transcript contigs into 86,714 non-redundant contigs

which became the basis for the remainder of the lncRNA

screen As a test of the completeness of the pan-tissue

beaver polyadenylated RNA transcriptome, we used a

benchmark set of 4014 genes (the mammalian

Bench-marking Universal Single-Copy Ortholog [BUSCO]

genes; see Methods) that had been previously validated

genome-sequenced mammalian species [24] We found

that 66% of the mammalian BUSCO genes had

high-confidence (E < 10− 5) matches to one or more contigs

in the Trinity-assembled, pan-tissue, beaver

polyadeny-lated RNA transcriptome

We filtered the 86,714 pan-tissue beaver transcript contigs

to identify probable lncRNA contigs using five filtering steps,

each shown in a row of Table 1: (1) identifying transcript

contigs that have annotated orthologs in other species; this

included identifying contigs with lncRNA orthologs (“known

lncRNAs”, which were further curated); (2) filtering based on

contigs’ coding potential score (p ≤ 0.01) as predicted based

on their hexamer sequence content and the length of and

coverage of the transcript by the longest Open Reading

Frame (ORF); (3) more stringently filtering based on contigs’

Coding Potential Assessment Tool (CPAT) score (q≤ 0.01;

see Methods) to obtain a set of high-confidence noncoding

contigs; (4) testing contigs for known protein domain

se-quences; and (5) aligning to the annotated reference beaver

genome assembly, to determine if a transcript contig was in

an untranslated region of a protein-coding gene At Step 2,

Additional file3Supplementary Data 1 for sequences) With

a more stringent cutoff to control for false discovery rate (Step 3), and including additional filtering steps (4) and (5),

we found a total of 187 probable lncRNA contigs: 40 non-coding transcript contigs that are orthologous to a known noncoding transcript in another species such as human or mouse (“known lncRNAs”) and 147 noncoding transcript contigs (see Table 1, bottom row) that appear to be novel from a species orthology standpoint (“novel lncRNAs”) (see Additional file4Supplementary Data 2 for sequences)

Length and secondary structure characterization of known and novel lncRNA contigs

To the extent that lncRNA biological function depends

on a sufficiently stable structural conformation [25], in order to quantitatively assess the noncoding contigs’ po-tential for function, we computationally modeled the secondary structures and obtained model-based Mini-mum Free Energy (MFE) estimates for all 187 (known and novel) contigs (see Methods) Both sets of lncRNAs had the expected inverse relationship between transcript (contig) length and MFE, though the relationship was weaker in the novel lncRNAs (Fig.1)

Overall, the transcript contigs for known lncRNAs were significantly (p < 10− 9; Kolmogorov-Smirnov test)

Whereas the annotated lncRNAs were in the range of 204–4691 nt in length (consistent with GENCODE [26]), the putative novel lncRNA contigs were all below 400 nt

in length This is consistent with previous RNA-seq-based lncRNA studies which have tended to produce shorter contigs (less than 400 nt) even with genome-guided assembly [27,28]

In terms of read-depth coverage level in the transcrip-tome assembly, the distributions for the two sets of non-coding transcript contigs were both right-skewed (Fig.3) Contigs with orthologs that are known noncoding tran-scripts (“known”) had higher average coverage depth (mode of 20.0, average of 369) than the noncoding tran-script contigs with no known orthologs (“novel”; mode of

Table 1 Contig retention through the screening pipeline for novel lncRNAs

Remaining

High confidence noncoding

(CPAT q < 0.01)

Columns as follows: “Step”, the name of the program or step in the screening pipeline; “% Contigs Eliminated”, the percentage of contigs from Column 4 of the previous row in the table that were eliminated in this step of the analysis pipeline; “# Contigs Eliminated”, the number of contigs corresponding to the

percentage in Column 2; “# Contigs Remaining”, the number of contigs remaining after the row’s filtering Step was applied The number of starting contigs before step 1 ( “Orthology analysis”) was 86,714

( a

) This includes the 40 beaver contigs that we identified that are orthologs of known noncoding transcripts in other species (Fig 9 , purple rectangle) The percentage shown in column “% Contigs Eliminated” is for that specific step (row) relative to the number of contigs before that step.

9.5, average of 19.4); the difference between the sets of

contigs was not as striking for coverage as for length

The putative novel lncRNAs map back to the draft beaver

genome

As a quality check, we aligned the 147 novel noncoding

contigs to a reference beaver genome assembly (Oregon

State University beaver genome assembly; see Methods)

Every transcript contig aligned with upwards of 90%

identity, and over 91% of putative novel lncRNA contigs

had an alignment equivalent to at least 70% of the

con-tig’s length (Additional file 1 Figure S1) One contig

non-overlapping alignments within 33 nucleotides of each

other on the draft genome, which may indicate excision

of an intron To further validate the 147 novel contigs,

we aligned them against a completely

independently-generated beaver genome assembly [7] using BLASTn (see Methods); 144 of them (all except contig72949.1, contig80019.1, and contig83657.1) aligned with a best-match E-value of less than 10− 18 Of the 144 aligned contigs, all of them had greater than 90% sequence mapped and 140 of them had greater than 95% sequence mapped

Novel lncRNAs in the American beaver

The novel lncRNAs as a group performed similarly to their annotated counterparts on the measures that we used to determine biological plausibility Eight candidate lncRNAs stood out, however, for having the strongest evidence across the various measures (Table 2) Five of

Fig 1 Noncoding transcript contigs ’ model-based structural stability is inversely correlated with length Marks indicate lncRNA contigs that have

no known orthologs ( “novel”; a) and that have known noncoding orthologs (“known”, b) The outlier in (b) is labeled by its known ortholog, XIST

Length (nt)

type

novel known

Fig 2 The lncRNA contigs with known orthologs are longer than

the novel lncRNA contigs Density distributions of contig lengths for

the 147 novel noncoding transcript contigs ( “novel”) and the 40

noncoding transcript contigs that are orthologous to known

noncoding transcripts ( “known”)

1000 10000

Contig Coverage Depth

type

novel known

Fig 3 In the pan-tissue transcriptome assembly, known lncRNA contigs had overall higher coverage levels than novel lncRNA contigs Density distributions of contig coverage depths for the 147 novel noncoding transcript contigs ( “novel”) and the 40 noncoding transcript contigs that are orthologous to known noncoding transcripts ( “known”) For both sets of noncoding transcript contigs, average depth of coverage in the assembly was not significantly correlated with contig length (Fig 5 )

these contigs were among the top ten contigs in terms

of at least length and MFE This concordance between

length and MFE is not surprising in light of the inverse

relationship between transcript length and secondary

structural stability (Fig 1) One novel lncRNA (Ccan_

OSU1_lncRNA_contig62060.1) was notable for having

two exons, as detected by gapped alignment to the

bea-ver genome All of the eight novel contigs had robust

ex-pression (⩾ 6.5) in at least one tissue, as measured by

Reads Per Kilobase of transcript per Million (RPKM)

(see Table2; Fig.4; Methods)

Interestingly, none of the eight lncRNAs were among

those contigs with the highest coverage This may be

ex-plained by the weakness of the relationship between

length and observed coverage of novel lncRNA

tran-scripts (Fig 5) Furthermore, among the novel

tran-scripts, the four contigs with exceptionally high coverage

had coverage that was, on average, 15-fold greater than

that of the rest of the contigs Additionally, all of these

contigs with exceptionally high coverage were under

250 nt long, while the ten longest novel lncRNAs were

over 300 nt

Beaver orthologs of known lncRNAs or known noncoding

transcript isoforms

Of the 40 lncRNA contigs for which a high-confidence

ortholog gene could be identified, the ortholog

annota-tions included 16 long noncoding RNA genes, 12

non-coding antisense RNAs, ten nonnon-coding isoforms of

protein-coding genes, and two sense-overlapping RNAs

(Table 3) The relatively large proportion (12 out of 40)

of antisense RNAs is consistent with a previous report

that antisense transcripts are highly prevalent in the

hu-man genome [29] The list of 16 lncRNA genes includes

beaver orthologs for well-known lncRNAs such as XIST

[2] (which was the longest of 187 high-confidence

lncRNA contigs at 3967 nt), maternally expressed gene 3

(MEG3) [30], terminal differentiation-induced

(Drosophila) long noncoding RNA bidirectional pro-moter (NIPBL-DT) [32]

To assess the possible functional coherence of the bea-ver lncRNAs with known orthologs, we analyzed KEGG biological pathway annotations for the human orthologs

of the Table3(ortholog-mapped) lncRNAs for statistical enrichment (see Methods) The analysis yielded seven significantly enriched (FDR < 0.05) pathways (Table 4) whose constituent genes are (in human) significantly correlated in expression with the query lncRNAs

Tissue-level expression of beaver lncRNAs

Following the lncRNA discovery phase of the analysis,

we used RNA-seq to analyze lncRNA levels in the 16 beaver tissues or anatomic structures (the same set of tissues from which we constructed the pooled transcrip-tome library): whole blood, brain, lung, liver, heart, stomach, intestine, skeletal muscle, kidney, spleen, ovar-ies, placenta, castor gland, tail skin, toe-webbing, and tongue For each of the 187 contigs1and in each of the

16 tissues, we estimated the transcript abundance in

Heatmap visualization of the tissue-specific expression profiles of the 147 novel (Fig 4) and 40 known (Fig 6) lncRNA contigs revealed both tissue-specific and ubiqui-tously expressed beaver lncRNAs

Among the 147 novel lncRNA contigs, several contigs are notable: contig84039.1 has extremely high (RPKM 1910) expression in castor sac relative to the other tis-sues (average RPKM of 64); contig81051.1 was ubiqui-tously expressed and had overall highest expression (average RPKM of 433); and a cluster of four contigs

Table 2 Novel lncRNA contigs with strongest evidence across multiple correlates

(RPKM) Length (nt) MFE (kcal/mol) Coverage BLASTn Alignment Length (%) Intronic

Underlined text indicates that a particular contig was in the top ten, among all novel lncRNA contigs, for the given column feature (i.e., length, MFE, coverage, or alignment length) The BLASTn alignment length is computed as 100×(length of alignment)/(length of contig) The sixth column (Intronic) reflects whether the contig’s alignment to the reference genome was gapped or not; a “yes” is indicative of a potential excised intron The last column, max (RPKM), is the maximum RPKM for the contig across all tissues and was not a criteria for inclusion in the table

1 In this subsection, in the interest of brevity, we identify contigs without the “Ccan_OSU1_lncRNA_” prefix.

(contig80136.1, contig83384.1, contig72740.1, and contig

83,657.1) are specifically expressed in stomach and

ney From a tissue lncRNA expression standpoint,

kid-ney and stomach clustered together in both the known

and novel lncRNA datasets, consistent with previous

findings from tissue transcriptome analysis [34] Brain

tissue was notable for having several tissue-specific

lncRNA contigs (contig76717.1, contig65642.1, and

contig43610.1) Finally, the heatmap analysis revealed that contig44966.1 is strongly expressed (over 20 RPKM)

in spleen and ovary (annotated as “gonad”), but not in other tissues (Fig.4, left panel, fifth row from bottom); it has no matches in the NCBI non-redundant nucleotide database, lncRNAdb [35], or in RNA Central [36], sug-gesting that if it is indeed a functional beaver lncRNA, it

is not known to be conserved in other rodents

Fig 4 Tissue-specific expression of novel lncRNAs in the American beaver Heatmap rows correspond to the 147 contigs and columns

correspond to the 16 tissues that were profiled Cells are colored by log 2 (1 + RPKM) expression level Rows and columns are separately ordered by hierarchical agglomerative clustering and cut-based sub-dendrograms are colored (arbitrary color assignment to sub-clusters) as a guide for visualization Rows are labeled with abbreviated contig names, e.g., contig4731.1 instead of Ccan_OSU1_lncRNA_contig4731.1

Fig 5 Contig average depth of read coverage in the assembly is not correlated with contig length Marks indicate contigs that do not have orthologs (a, 147 contigs) or that are orthologous to known noncoding transcripts (b, 40 contigs) The outlier in (b) is labeled by its known ortholog, XIST

Table 3 Beaver noncoding contigs that are probable orthologs of known lncRNAs or noncoding transcripts

Symbol;

annotation

Contig Species with

ortholog hits

Human Ensembl Gene ID

AC037459.2;

(antisense to

CCAR2)

Ccan_OSU1_

lncRNA_

contig74544.1

Homo sapiens ENSG00000253200 CCAR2 lncRNA (cell cycle and apoptosis

regulator 2)

8.0 10−46 89 155

AC019068.1;

antisense

Ccan_OSU1_

lncRNA_

contig10709.1

Homo sapiens ENSG00000233611 AC079135.1 gene, antisense lncRNA (TPA

-predicted)

2.4 10−12 77.6 143

AC083843.1 Ccan_OSU1_

lncRNA_

contig47288.1

Homo sapiens ENSG00000253433 AC083843.1 gene, lincRNA (TPA

-predicted)

7.7 10−13 88.4 69

AC095055.1

(antisense to

SH3D19)

Ccan_OSU1_

lncRNA_

contig41532.1

Homo sapiens ENSG00000270681 SH3D19 antisense noncoding RNA (SH3

domain containing 19)

8.1 10− 58 82.9 274

AC116667.1;

(antisense to

ZFHX3)

Ccan_OSU1_

lncRNA_

contig71613.1

Homo sapiens ENSG00000271009 ZFHX3 antisense (zinc finger homeobox 3) 1.8 10−47 83.6 231

AL161747.2;

(antisense to

SALL2)

Ccan_OSU1_

lncRNA_

contig44345.1

Homo sapiens ENSG00000257096 SALL2 lncRNA (spalt-like transcription

factor 2)

7.5 10−68 84.4 288

AP000233.2 Ccan_OSU1_

lncRNA_

contig22249.1

Homo sapiens ENSG00000232512 AP000233.2 gene lincRNA (TPA

-predicted)

9.0 10−5 100 31

AP003068.1;

(antisense to

VPS51)

Ccan_OSU1_

lncRNA_

contig24716.1

Homo sapiens, Mus musculus, Bos taurus

ENSG00000254501 VPS51 antisense (vacuolar protein sorting

51)

AP003068.1;

(antisense to

VPS51)

Ccan_OSU1_

lncRNA_

contig55707.1

Mus musculus, Homo sapiens, Gallus gallus

ENSG00000254501 VPS51 antisense/reverse strand (vacuolar

protein sorting 51)

1.7 10−83 92 226

CTA-204B4.6 † Ccan_OSU1_

lncRNA_

contig29141.1

Homo sapiens ENSG00000259758 CTA204B4.6 gene lincRNA (TPA

-predicted)

6.2 10−

120 83.5 491

CTA-204B4.6 Ccan_OSU1_

lncRNA_

contig30023.1

Homo sapiens ENSG00000259758 CTA204B4.6 gene lincRNA (TPA

-predicted)

2.1 10−

129 94.5 308

DNM3OS;

(antisense to

DNM3)

Ccan_OSU1_

lncRNA_

contig78034.1

Homo sapiens;

various primates

ENSG00000230630 DNM3OS (DNM3 opposite strand/

antisense RNA) lncRNA

3.4 10−69 89.8 216

GNB4; lncRNA

isoform*

Ccan_OSU1_

lncRNA_

contig55083.1

Homo sapiens ENSG00000114450 GNB4 (guanine nucleotide binding protein

(G protein), beta polypeptide 4)

6.4 10−38 78.8 287

AC007038.2;

(antisense to

KANSL1L)

Ccan_OSU1_

lncRNA_

contig54664.1

Homo sapiens, Mus musculus

ENSG00000272807 KANSL1L antisense transcript (KAT8

regulatory NSL complex subunit 1-like)

1.1 10−40 92 125

KCNA3;

noncoding

isoform

Ccan_OSU1_

lncRNA_

contig27553.1

Homo sapiens, Mus musculus

ENSG00000177272 KCNA3 lncRNA (potassium voltage-gated

channel, shaker-related subfamily, member 3)

2.3 10−

139 85.5 502

KCNA3;

noncoding

isoform

Ccan_OSU1_

lncRNA_

contig29471.1

Homo sapiens ENSG00000177272 KCNA3 lncRNA (potassium voltage-gated

channel, shaker-related subfamily, member 3)

1.8 10−70 78.7 475

KCNA3;

noncoding

isoform

Ccan_OSU1_

lncRNA_

contig79757.1

Homo sapiens ENSG00000177272 KCNA3 lncRNA (potassium voltage-gated

channel, shaker-related subfamily, member 3)

7.6 10−31 80.2 197

KCNA3;

noncoding

isoform

Ccan_OSU1_

lncRNA_

contig81530.1

Homo sapiens, Mus musculus

ENSG00000177272 KCNA3 lncRNA (potassium voltage-gated

channel, shaker-related subfamily, member 3)

7.1 10−61 87.7 211

LINC01355 Ccan_OSU1_

lncRNA_

contig54147.1

Homo sapiens ENSG00000261326 LINC01355 lncRNA 1.0 10− 85 87.5 295